25,026 results match your criteria protein peaks

H4K20me3 marks distal intergenic and repetitive regions in human mature spermatozoa.

Development 2021 Aug 3;148(15). Epub 2021 Aug 3.

Clinic of Urology, Pediatric Urology and Andrology, Justus-Liebig University Giessen, 35392 Giessen, Germany.

Sperm histones represent an essential part of the paternally transmitted epigenome, but uncertainty exists about the role of those remaining in non-coding and repetitive DNA. We therefore analyzed the genome-wide distribution of the heterochromatic marker H4K20me3 in human sperm and somatic (K562) cells. To specify the function of sperm histones, we compared all H4K20me3-containing and -free loci in the sperm genome. Read More

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Elucidating the chemical and structural composition of breast cancer using Raman micro-spectroscopy.

EXCLI J 2021 2;20:1118-1132. Epub 2021 Jul 2.

Engineering Department, Faculty of Science and Technology, Lancaster University, Lancaster LA1 4YW, U.K.

The current gold standard for breast cancer (BC) diagnosis is the histopathological assessment of biopsy samples. However, this approach limits the understanding of the disease in terms of biochemical changes. Raman spectroscopy has demonstrated its potential to provide diagnostic information and facilitate the prediction of the biochemical progression for different diseases in a rapid non-destructive manner. Read More

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Transcriptome-wide mA profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation.

BMC Genomics 2021 Aug 3;22(1):588. Epub 2021 Aug 3.

College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.

Background: Cryopreservation induces transcriptomic and epigenetic modifications that strongly impairs sperm quality and function, and thus decrease reproductive performance. N-methyladenosine (mA) RNA methylation varies in response to stress and has been implicated in multiple important biological processes, including post-transcriptional fate of mRNA, metabolism, and apoptosis. This study aimed to explore whether cryopreservation induces mA modification of mRNAs associated with sperm energy metabolism, cryoinjuries, and freezability. Read More

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Preliminary exploration on the serum biomarkers of bloodstream infection with carbapenem-resistant Klebsiella pneumoniae based on mass spectrometry.

J Clin Lab Anal 2021 Jul 31:e23915. Epub 2021 Jul 31.

College of Medical Technology, Xuzhou Medical University, Xuzhou, China.

Background: Carbapenem-resistant K. pneumoniae (CRKP) bloodstream infections (BSI) must be rapidly identified to improve patient survival rates. This study investigated a new mass spectrometry-based method for improving the identification of CRKP BSI and explored potential biomarkers that could differentiate CRKP BSI from sensitive. Read More

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Disruption of NIPBL/Scc2 in Cornelia de Lange Syndrome provokes cohesin genome-wide redistribution with an impact in the transcriptome.

Nat Commun 2021 07 27;12(1):4551. Epub 2021 Jul 27.

Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain.

Cornelia de Lange syndrome (CdLS) is a rare disease affecting multiple organs and systems during development. Mutations in the cohesin loader, NIPBL/Scc2, were first described and are the most frequent in clinically diagnosed CdLS patients. The molecular mechanisms driving CdLS phenotypes are not understood. Read More

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Epitranscriptomic Analysis of m6A Methylome After Peripheral Nerve Injury.

Front Genet 2021 9;12:686000. Epub 2021 Jul 9.

Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China.

N6-methyladenosine (m6A) is one of the most plentiful internal RNA modifications, especially in eukaryotic messenger RNA (mRNA), which plays pivotal roles in the regulation of mRNA life cycle and nerve development. However, the mRNA m6A methylation pattern in peripheral nervous injury (PNI) has not been investigated. In this study, sciatic nerve samples were collected from 7 days after sciatic nerve injury (SNI) and control rats. Read More

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The Role of INAPERTURATE POLLEN1 as a Pollen Aperture Factor Is Conserved in the Basal Eudicot (Papaveraceae).

Front Plant Sci 2021 7;12:701286. Epub 2021 Jul 7.

Department of Botany, Faculty of Sciences, University of Granada, Granada, Spain.

Pollen grains show an enormous variety of aperture systems. What genes are involved in the aperture formation pathway and how conserved this pathway is in angiosperms remains largely unknown. () encodes a protein of unknown function, essential for aperture formation in Arabidopsis, rice and maize. Read More

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Differential mutation profile of SARS-CoV-2 proteins across deceased and asymptomatic patients.

Chem Biol Interact 2021 Jul 23;347:109598. Epub 2021 Jul 23.

Clinical and Applied Genomics (CAG) Laboratory, Department of Biological Sciences, Aliah University, Kolkata, India. Electronic address:

Background: The SARS-CoV-2 infection has spread at an alarming rate with many places showing multiple peaks in incidence. Present study analyzes a total of 332 SARS-CoV-2 genome sequences from 114 asymptomatic and 218 deceased patients from twenty-one different countries to assess the mutation profile therein in order to establish the correlation between the clinical status and the observed mutations.

Methods: The mining of mutations was carried out using the GISAID CoVSurver (www. Read More

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Detection of structural and conformational changes in ALS-causing mutant profilin-1 with hydrogen/deuterium exchange mass spectrometry and bioinformatics techniques.

Metab Brain Dis 2021 Jul 24. Epub 2021 Jul 24.

Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran.

The hydrogen/deuterium exchange (HDX) is a reliable method to survey the dynamic behavior of proteins and epitope mapping. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is a quantifying tool to assay for HDX in the protein of interest. We combined HDX-MALDI-TOF MS and molecular docking/MD simulation to identify accessible amino acids and analyze their contribution into the structural changes of profilin-1 (PFN-1). Read More

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NMR Spectroscopy for Protein Higher Order Structure Similarity Assessment in Formulated Drug Products.

Molecules 2021 Jul 13;26(14). Epub 2021 Jul 13.

Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA.

Peptide and protein drug molecules fold into higher order structures (HOS) in formulation and these folded structures are often critical for drug efficacy and safety. Generic or biosimilar drug products (DPs) need to show similar HOS to the reference product. The solution NMR spectroscopy is a non-invasive, chemically and structurally specific analytical method that is ideal for characterizing protein therapeutics in formulation. Read More

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Expression of DDX11 and DNM1L at the 12p11 Locus Modulates Systemic Lupus Erythematosus Susceptibility.

Int J Mol Sci 2021 Jul 16;22(14). Epub 2021 Jul 16.

Rheumatology Service, Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Reina Sofia Hospital, University of Cordoba, 14004 Cordoba, Spain.

Objectives: This study employed genetic and functional analyses using OASIS meta-analysis of multiple existing GWAS and gene-expression datasets to identify novel SLE genes.

Methods: Four hundred and ten genes were mapped using SNIPPER to 30 SLE GWAS loci and investigated for expression in three SLE GEO-datasets and the Cordoba GSE50395-dataset. Blood eQTL for significant SNPs in SLE loci and STRING for functional pathways of differentially expressed genes were used. Read More

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The Mode of SN38 Derivatives Interacting with Nicked DNA Mimics Biological Targeting of Topo I Poisons.

Int J Mol Sci 2021 Jul 12;22(14). Epub 2021 Jul 12.

National Medicines Institute, 00-725 Warsaw, Poland.

The compounds 7-ethyl-9-(-methylamino)methyl-10-hydroxycamptothecin () and 7-ethyl-9-(-morpholino)methyl-10-hydroxycamptothecin () are potential topoisomerase I poisons. Moreover, they were shown to have favorable anti-neoplastic effects on several tumor cell lines. Due to these properties, the compounds are being considered for advancement to the preclinical development stage. Read More

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How to Obtain a Mega-Intestine with Normal Morphology: In Silico Modelling of Postnatal Intestinal Growth in a Cd97-Transgenic Mouse.

Int J Mol Sci 2021 Jul 8;22(14). Epub 2021 Jul 8.

Interdisciplinary Institute for Bioinformatics (IZBI), Leipzig University, 04107 Leipzig, Germany.

Intestinal cylindrical growth peaks in mice a few weeks after birth, simultaneously with crypt fission activity. It nearly stops after weaning and cannot be reactivated later. Transgenic mice expressing / in the intestinal epithelium develop a mega-intestine with normal microscopic morphology in adult mice. Read More

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Genomic investigation of colour polymorphism and phylogeographic variation among populations of black-headed bulbul (Brachypodius atriceps) in insular southeast Asia.

Mol Ecol 2021 Jul 23. Epub 2021 Jul 23.

Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA.

Intraspecific polymorphism in birds, especially plumage colour polymorphism, and the mechanisms that control it are an area of active research in evolutionary biology. The black-headed bulbul (Brachypodius atriceps) is a polymorphic species with two distinct morphs, yellow and grey. This species inhabits the mainland and virtually all continental islands of Southeast Asia where yellow morphs predominate, but on two islands in the Sunda region, Bawean and Maratua, grey morphs are common or exclusive. Read More

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Developing Two Rapid Protein Extraction Methods Using Focused-Ultrasonication and Zirconia-Silica Beads for Filamentous Fungi Identification by MALDI-TOF MS.

Front Cell Infect Microbiol 2021 6;11:687240. Epub 2021 Jul 6.

Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

Filamentous fungi identification by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been challenging due to the lack of simple and rapid protein extraction methods and insufficient species coverage in the database. In this study, we created two rapid protein extraction methods for filamentous fungi: a one-step zirconia-silica beads method (ZSB) and a focused-ultrasonication method (FUS). The identification accuracy of two methods were evaluated with the VITEK MS, as well as number of spectra peaks and signal-to-noise ratio (S/N) with M-Discover 100 MALDI-TOF MS compared to the routine method. Read More

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Bacterial Sub-Species Typing Using Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry: What Is Promising?

Curr Issues Mol Biol 2021 Jul 20;43(2):749-757. Epub 2021 Jul 20.

University of Queensland Centre for Clinical Research, The University of Queensland, Herston, Brisbane, QLD 4029, Australia.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used for bacterial identification. It would be highly beneficial to also be able to use the technology as a fast way to detect clinically relevant clones of bacterial species. However, studies to this aim have often had limited success. Read More

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Sum frequency generation spectroscopy of the attachment disc of a spider.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Jul 9;263:120161. Epub 2021 Jul 9.

School of Electronic and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK.

The pyriform silk of the attachment disc of a spider was studied using infrared-visible vibrational sum frequency generation (SFG) spectroscopy. The spider can attach dragline and radial lines to many kinds of substrates in nature (concrete, alloy, metal, glass, plant branches, leaves, etc.) with the attachment disc. Read More

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Use of a Daratumumab-Specific Immunofixation Assay to Assess Possible Immunotherapy Interference at a Major Cancer Center: Our Experience and Recommendations.

J Appl Lab Med 2021 Jul 22. Epub 2021 Jul 22.

Clinical Chemistry Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.

Background: The incorporation of monoclonal antibodies, such as daratumumab, into multiple myeloma treatment regimens has led to the issue of false-positive interference in both serum protein electrophoresis (SPEP) and immunofixation (IF). The Hydrashift assay removes daratumumab interference from IF, allowing for correct interpretation. Here, we retrospectively examined the use of the Hydrashift assay at a large cancer center and provide guidelines on its most appropriate use. Read More

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Determining the Diastereoselectivity of the Formation of Dipeptidonucleotides by NMR Spectroscopy.

Chemistry 2021 Jul 22. Epub 2021 Jul 22.

University of Stuttgart, Chemistry, GERMANY.

Proteins are composed of l-amino acids, but nucleic acids and most oligosaccharides contain d-sugars as building blocks. It is interesting to ask whether this is a coincidence or a consequence of the functional interplay of these biomolecules. One reaction that provides an opportunity to study this interplay is the formation of phosphoramidate-linked peptido RNA from amino acids and ribonucleotides in aqueous condensation buffer. Read More

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SARS-CoV-2 Receptor Binding Domain as a Stable-Potential Target for SARS-CoV-2 Detection by Surface-Enhanced Raman Spectroscopy.

Sensors (Basel) 2021 Jul 5;21(13). Epub 2021 Jul 5.

Department of Physics, College of Science, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia.

In this work, we report a new approach for detecting SARS-CoV-2 RBD protein (RBD) using the surface-enhanced Raman spectroscopy (SERS) technique. The optical enhancement was obtained thanks to the preparation of nanostructured Ag/Au substrates. Fabricated Au/Ag nanostructures were used in the SERS experiment for RBD protein detection. Read More

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Immunoassay of SARS-CoV-2 nucleocapsid proteins using novel red emission-enhanced carbon dot-based silica spheres.

Analyst 2021 Jul 20. Epub 2021 Jul 20.

Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.

It is imminent to develop a new type of rapid COVID-19 detection method with high sensitivity. Here, we used novel red emission-enhanced carbon dot (CD)-based silica (RCS) spheres as the signals of lateral flow immunochromatography (LFI) to ultrasensitively detect novel severe acute respiratory syndrome coronavirus 2 nucleocapsid proteins (SARS-CoV-2 NPs). The red emission of CDs can be enhanced and enriched in silica spheres by a simple way. Read More

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Synthesis of pH and Glucose Responsive Silk Fibroin Hydrogels.

Int J Mol Sci 2021 Jul 1;22(13). Epub 2021 Jul 1.

National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, Suzhou 215123, China.

Silk fibroin (SF) has attracted much attention due to its high, tunable mechanical strength and excellent biocompatibility. Imparting the ability to respond to external stimuli can further enhance its scope of application. In order to imbue stimuli-responsive behavior in silk fibroin, we propose a new conjugated material, namely cationic SF (CSF) obtained by chemical modification of silk fibroin with ε-Poly-(L-lysine) (ε-PLL). Read More

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Geomicrobiological Heterogeneity of Lithic Habitats in the Extreme Environment of Antarctic Nunataks: A Potential Early Mars Analog.

Front Microbiol 2021 2;12:670982. Epub 2021 Jul 2.

Centro de Astrobiología, CSIC-INTA, Madrid, Spain.

Nunataks are permanent ice-free rocky peaks that project above ice caps in polar regions, thus being exposed to extreme climatic conditions throughout the year. They undergo extremely low temperatures and scarcity of liquid water in winter, while receiving high incident and reflected (albedo) UVA-B radiation in summer. Here, we investigate the geomicrobiology of the permanently exposed lithic substrates of nunataks from Livingston Island (South Shetlands, Antarctic Peninsula), with focus on prokaryotic community structure and their main metabolic traits. Read More

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Biosynthesis of UDP-2-acetamido-4-formamido-2,4,6-trideoxy-hexose by WekG, WekE, WekF, and WekD: Enzymes in the Wek pathway responsible for O-antigen Assembly in Escherichia coli O119.

Carbohydr Res 2021 Sep 7;507:108388. Epub 2021 Jul 7.

TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China; Key Laboratory of Microbial Functional Genomics, Tianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China. Electronic address:

Considering the importance of bacterial glycoconjugates on virulence and host mimicry, there is a need to better understand the biosynthetic pathways of these unusual sugars to identify critical targets involved in bacterial pathogenesis. In this report, we describe the cloning, overexpression, purification, and biochemical characterization of the four central enzymes in the biosynthesis pathway for UDP-2-acetamido-4-formamido-2,4,6-trideoxy-hexose, WekG, WekE, WekF, and WekD. Product peaks from enzyme-substrate reactions were detected by using a combination of capillary electrophoresis (CE) and electrospray ionization-mass spectrometry (ESI-MS). Read More

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September 2021

H4K20me3 marks distal intergenic and repetitive regions in human mature spermatozoa.

Development 2021 Jul 16. Epub 2021 Jul 16.

Clinic of Urology, Pediatric Urology and Andrology, Justus-Liebig University Giessen, 35392 Giessen, Germany.

Sperm histones (SHs) represent an essential part of the paternally transmitted epigenome, but uncertainty exists about the role of those remaining in non-coding and repetitive DNA. We therefore analyzed the genome-wide distribution of the heterochromatic marker H4K20me3 in human sperm and somatic (K562) cells. To specify the function of SHs, we compared all H4K20me3-containing and -free loci in sperm genome. Read More

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Engineered promoter-switched viruses reveal the role of poxvirus maturation protein A26 as a negative regulator of viral spread.

J Virol 2021 Jul 14:JVI0101221. Epub 2021 Jul 14.

Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, GU2 7XH, United Kingdom.

Vaccinia virus produces two types of virions known as single-membraned intracellular mature virus (MV) and double-membraned extracellular enveloped virus (EV). EV production peaks earlier when initial MV are further wrapped and secreted to spread infection within the host. However, late during infection MV accumulate intracellularly and become important for host-to-host transmission. Read More

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Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters.

Struct Dyn 2021 Jul 8;8(4):044701. Epub 2021 Jul 8.

Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, USA.

Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks-diffuse scattering-is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. Read More

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[Diagnostic value of FNDC5 in patients with subclinical diabetic cardiomyopathy].

Zhonghua Xin Xue Guan Bing Za Zhi 2021 Jul 24;49(7):687-693. Epub 2021 Jul 24.

Department of Endocrinology, Third Affiliated Hospital of Soochow University, Suzhou 213000, China.

To estimate the diagnostic value of fibronectin type Ⅲ-domain containing protein 5 (FNDC5) in subclinical diabetic cardiomyopathy. A total of 94 patients with type 2 diabetes (T2DM), who were hospitalized from April 2018 to June 2019 in the Third Affiliated Hospital of Soochow University, were enrolled in this study. Patients were divided into T2DM with cardiac dysfunction (subclinical DCM) group (=47) and T2DM without cardiac dysfunction (non-DCM) group (=47) according to echocardiography and gated myocardial perfusion imaging results. Read More

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Isotope-Edited Amide II Mode: A New Label for Site-Specific Vibrational Spectroscopy.

J Phys Chem Lett 2021 Jul 13;12(28):6634-6638. Epub 2021 Jul 13.

The Alexander Silberman Institute of Life Sciences. Department of Biological Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190400, Israel.

Vibrational spectroscopy is a powerful tool used to analyze biological and chemical samples. However, in proteins, the most predominant peaks that arise from the backbone amide groups overlap one another, hampering site-specific analyses. Isotope editing has provided a robust, noninvasive approach to overcome this hurdle. Read More

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Tissue-specific 5-hydroxymethylcytosine landscape of the human genome.

Nat Commun 2021 07 12;12(1):4249. Epub 2021 Jul 12.

State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.

5-Hydroxymethylcytosine (5hmC) is an important epigenetic mark that regulates gene expression. Charting the landscape of 5hmC in human tissues is fundamental to understanding its regulatory functions. Here, we systematically profiled the whole-genome 5hmC landscape at single-base resolution for 19 types of human tissues. Read More

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